Biology subjects

Diaz, J. M.

Publications and source records attributed to Diaz, J. M..

10 recordsLinked to original sources

bioRxiv2026

Alkaline phosphatase activity supports heterotrophic carbon acquisition in a coastal time series site and a representative marine bacterium

Phosphorus is a vital nutrient required for the functioning of living organisms. In aquatic environments, dissolved inorganic phosphate is considered its most bioavailable form. However, phosphate can be scarce, which has the potential to limit microbial metabolism and ecosystem functioning. To overcome phosphate scarcity, microbes produce alkaline phosphatase (AP) to access dissolved organic phosphorus (DOP). Here, we conducted a year-long study of alkaline phosphatase activity (APA) at the Ellen Browning Scripps Memorial Pier, a nutrient-rich coastal site. APA was observed throughout the year despite phosphate-replete conditions, suggesting that the role of APs in microbial nutrition is not completely understood. We tested the hypothesis that APA may promote acquisition of organic carbon liberated from DOP hydrolysis by growing the heterotrophic marine bacterium Ruegeria pomeroyi on three DOP compounds as sole carbon sources and assessing APA. Controlling for carbon concentration, all DOP sources supported growth, but at lower levels than glucose, with the highest growth observed on glucose-6-phosphate (G6P), followed by adenosine monophosphate (AMP) and adenosine triphosphate (ATP). Moreover, cell-specific APA was significantly enhanced in carbon-deplete conditions and during growth on G6P, relative to cultures grown on replete glucose or nucleotides. These findings suggest alkaline phosphatases (APs) are part of a generic carbon stress response and likely play a role in acquiring certain forms of organic carbon by R. pomeroyi, with implications for other taxa. Overall, this study helps advance the current state of knowledge regarding microbial phosphorus cycling and carbon utilization in aquatic environments.

microbiology↗

bioRxiv2025

Extracellular superoxide production is a widespread photoacclimation strategy in phytoplankton

Phytoplankton control the habitability of Earth. These photosynthetic microorganisms serve as the base of marine food webs, produce approximately half of the planets oxygen, and regulate climate by sequestering carbon dioxide from the atmosphere. As global changes accelerate through the Anthropocene, phytoplankton communities face multiple stressors, including warming, shifting patterns in ocean circulation and structure, and associated perturbations in levels of light exposure. The health and functioning of the oceans depends on phytoplankton community responses to these stressors; however, the physiological processes involved in light stress are not fully understood. Here, we surveyed sixteen representative phytoplankton and show that most produce extracellular superoxide, an otherwise damaging reactive oxygen species, as a widespread strategy to acclimate to light stress. Indeed, all species regulated extracellular superoxide production as a function of light exposure, which was modeled with a modified photosynthesis-irradiance (PE) curve. Furthermore, the flavoenzyme inhibitor DPI quenched extracellular superoxide production and lead to declines in viability and photosynthetic health in thirteen out of sixteen species. The negative effect of DPI on photosynthetic health was stronger with increasing light, consistent with inhibition of a photoprotective process. Taken together, these results support the hypothesis that phytoplankton mitigate light stress through enzyme-mediated production of extracellular superoxide. These results imply that daytime rates of biological superoxide production in the marine environment are substantially underestimated by dark measurements. Furthermore, phytoplankton photoacclimation may alter superoxide production rates in future oceans impacted by changes in water column structure and light exposure.

microbiology↗

bioRxiv2025

Atypical phosphatases drive dissolved organic phosphorus utilization by phosphorus-stressed phytoplankton in the California Current Ecosystem

In the ocean, dissolved organic phosphorus (DOP) supports the health and productivity of marine phytoplankton, a phenomenon most often investigated under inorganic phosphate (Pi) scarcity. However, microbial DOP acquisition occurring in Pi replete ocean environments remains poorly understood. Here, we conducted a combination of nutrient addition experiments, alkaline phosphatase (AP) rate measurements, and metatranscriptomics analyses along an onshore-to-offshore gradient in the California Current Ecosystem (CCE), a relatively Pi-rich upwelling region. We found that AP activity (APA) and eukaryotic transcripts for DOP utilization were present throughout the CCE. In bottle incubations, APA was upregulated in response to iron (Fe) and nitrogen (N) additions. Major contributors to these trends included atypical alkaline phosphatases (APaty) of diatoms in the coastal upwelling area, and unclassified non-cytoplasmic P-diesterases (PDEnc) of multiple eukaryotic taxa in the offshore regime. APA and gene expression dynamics were not coupled to phytoplankton growth, suggesting that these organisms experience underlying P stress, a state of cellular metabolism caused by Pi scarcity, even in regions primarily growth-limited by other elements. While APaty and PDEnc were highly abundant among the microbial community phosphatase pool, these genes were missing from a widely used annotation database, highlighting the importance of manual curation for the detection of these atypical and unclassified proteins. Altogether, these results emphasize the functional diversity of phosphatases sustaining microbial community health in diverse and productive marine habitats.

microbiology↗

bioRxiv2024

Resting After Learning Facilitates Memory Consolidation and Reverses Spatial Reorientation Impairments in 'New Surroundings' in 3xTg-AD Mice

Sleep is an essential component of productive memory consolidation and waste clearance, including pathology associated with Alzheimers disease (AD). Facilitation of sleep decreases A{beta} and tau accumulation and is important for the consolidation of spatial memories. We previously found that 6-month female 3xTg-AD mice were impaired at spatial reorientation. Given the association between sleep and AD, we assessed the impact of added rest on impaired spatial reorientation that we previously observed. We randomly assigned 3xTg-AD mice to a rest (n=7; 50 min pre- & post-task induced rest) or a non-rest group (n=7; mice remained in the home cage pre- & post-task). Mice in both groups were compared to non-Tg, age-matched, non-rest controls (n=6). To confirm that our sleep condition induced sleep, we performed the same experiment with rest sessions for both 3xTg-AD and non-Tg mice (n=6/group) implanted with recording electrodes to capture local field potentials (LFPs), which were used to classify sleep states. Markers of pathology were also assessed in the parietal-hippocampal network, where we previously showed pTau positive cell density predicted spatial reorientation ability (pTau, 6E10, M78, and M22). However, we found that 3xTg-AD rest mice were not impaired at spatial reorientation compared to non-Tg mice and performed better than 3xTg-AD non-rest mice (replicating our previous work). This recovered behavior persisted despite no change in the density of pathology positive cells. Thus, improving sleep in early stages of AD pathology offers a promising approach for facilitating memory consolidation and improving cognition.

neuroscience↗

bioRxiv2023

Energy flux couples sulfur isotope fractionation to proteomic and metabolite profiles in Desulfovibrio vulgaris

Microbial sulfate reduction is central to the global carbon cycle and the redox evolution of Earths surface. Tracking the activity of sulfate reducing microorganisms over space and time relies on a nuanced understanding of stable sulfur isotope fractionation in the context of the biochemical machinery of the metabolism. Here we link the magnitude of stable sulfur isotopic fractionation to proteomic and metabolite profiles under different cellular energetic regimes. When energy availability is limited, cell specific sulfate respiration rates and net sulfur isotope fractionation inversely co-vary. Beyond net S isotope fractionation values, we also quantified shifts in protein expression, abundances and isotopic composition of intracellular S metabolites, and lipid structures and lipid/water H isotope fractionation values. These coupled approaches reveal which protein abundances shift directly as a function of energy flux, those that vary minimally, and those that may vary independent of energy flux and likely do not contribute to shifts in S-isotope fractionation. By coupling the bulk S-isotope observations with quantitative proteomics, we provide novel constraints for metabolic isotope models. Together, these results lay the foundation for more predictive metabolic fractionation models, alongside interpretations of environmental sulfur and sulfate reducer lipid-H isotope data.

microbiology↗

bioRxiv2022

Membrane Retrieval after Immediately Releasable Pool (IRP) Exocytosis is produced by Dynamin-Dependent and Dynamin-Independent Mechanisms

The importance of the immediately releasable pool (IRP) of vesicles was proposed to reside in the maintenance of chromaffin cell secretion during the firing of action potentials at basal physiological frequencies. To accomplish this duty, IRP should be replenished as a function of time. We have previously reported that an action potential-like stimulus (APls) triggers the release of {bsim}50% IRP, followed by a fast dynamin-dependent endocytosis and an associated rapid replenishment process. In this work we investigated the endocytosis and IRP replenishment produced after the exocytosis of variable IRP fractions in mice primary chromaffin cell cultures. Exocytosis and endocytosis were estimated by membrane capacitance measurements obtained in patch-clamped cells. In addition to the dynamin-dependent fast endocytosis activated after the application of APls or 5 ms squared depolarizations, we found that depolarizations lasting 25-50 ms, which release >80% of IRP, are related with a fast dynamin-independent, Ca2+- and protein kinase C (PKC)-dependent endocytosis (time constant < 1 s). PKC inhibitors, such as staurosporine, bisindolylmaleimide XI and prolonged treatments with high concentrations of phorbol esters, reduced and decelerated this endocytosis. Additionally, we found that the inhibition of PKC also abolished a slow component of replenishment (time constant {bsim}8 s) observed after total IRP exocytosis. Therefore, our results suggest that PKC contributes to the coordination of membrane retrieval and vesicle replenishment mechanisms that occur after the complete exocytosis of IRP.

physiology↗

bioRxiv2021

Modelling the effects of land use on mangroves in a RAMSAR site of Panama

The role of mangroves as pivotal providers of ecosystem services has been widely acknowledged. In Latin America, mangroves play an important role in traditional coastal livelihoods, but the growing economy of these nations demands the expansion of land for development, putting pressure in ecosystems such as mangroves. Here we examine the impact of land use activities on mangroves in the Gulf of Montijo, a RAMSAR site located in the Pacific coast of Panama. Spatial information of land use was analysed, ground-truthed and classified into agriculture, aquaculture and coastal development, and subsequently ranked according to estimated level of impact on mangroves based on 27 interviews with local informants. We developed a spatially-referenced cumulative impact model of human activities on mangroves. Results showed that despite the protection status of the Gulf of Montijo, its mangrove forests are affected by localised human activities, dominated by agriculture. Given the importance of fishing for local livelihoods, evaluating the effects of agriculture, rice in particular, on mangroves and their associated fauna will be essential for the sustainable management of this RAMSAR site.

ecology↗

bioRxiv2021

Identifying nearshore nursery habitats for sharks in the Eastern Tropical Pacific from fisheries landings and interviews

The Eastern Tropical Pacific (ETP) comprising the coasts of Costa Rica, Panama, Colombia and Ecuador, represents an area of high marine biodiversity that supports productive fisheries and acts as an important migratory corridor for many marine species. Despite its biological importance, the ETP is understudied and lacks sufficient data for science-based fisheries management and conservation decision-making. This study aims to consolidate understanding of the current and historical distribution of sharks and mobulid rays in the ETP. We used interviews of coastal community stakeholders to document traditional knowledge of shark and mobulid ray species and distributions. We also analysed small-scale fisheries landings data, where available, to quantify local exploitation patterns and the importance of sharks and rays in small-scale fisheries catches. All shark species landed in the dominant nearshore gillnet fishery show very low mean individuals weights (<5 kg), indicating that the fisheries are dominated by juveniles, captured. Aside from smooth-hounds (Mustelus spp.), the scalloped hammerhead shark, Sphyrna lewini, is the most frequently landed shark species in the region by weight and number, with peaks in abundance between April - July. From 132 interviews in 51 communities across the three countries, and landings data from two small-scale fisheries sites, we identified 41 sites in 12 broad geographical zones as important shark nursery habitats. Of these sites, 68% were associated closely with large mangrove systems of the ETP, highlighting the importance of this habitat for shark life history. No patterns were seen in the occurrence or distribution of mobulid rays in coastal areas. Marine protected areas and responsible fishing zones cover 37% of identified nursery habitats in the ETP, 30% in Costa Rica, 48% in Panama and 30% in Colombia. These findings provide an important benchmark of the conservation status of sharks in the ETP and allow for the prioritisation of research and policy-making.

ecology↗

bioRxiv2021

Identifying priority areas for research and conservation of the largetooth sawfish Pristis pristis in Colombia and Panama

Sawfishes are considered one of the most endangered families of fishes in the world. Their diadromous ecology and vulnerability to fishing nets have brought most populations to the brink of collapse. Conservation of the surviving populations is hindered by the paucity of historic and contemporary catch and observational records, and assessments of suitable coastal and riverine habitats. Colombia and Panama are two of 14 countries considered as a high priority for the development of species-specific national legal protection of the critically endangered largetooth sawfish (Pristis pristis). To construct a baseline for the temporal and spatial distribution of the largetooth sawfish in Colombia and Panama, we collected historical records from museum databases and from literature over the past century, analysed available small-scale fisheries landings databases, and conducted interviews with fish workers in 38 locations across both countries. We found 257 records of sawfish occurrences across both countries between 1896 and 2015, with 69% of the records before the year 2000. The declining trend in the frequency of observations was corroborated by fishers, who reported fewer sawfish catches over the last 20 years. Using kernel density estimation of recent encounter locations, we identify potential hotspots that may represent extant populations of sawfish. These locations are broadly characterized by their remoteness and high mangrove forest cover. Given the length and cultural diversity of the Pacific coastlines of Colombia and Panama, and the inaccessibility of many of the communities, our findings provide important guidance to target rapid conservation and fisheries interventions to priority areas. We suggest that the relative success of community-managed fishing areas in the region makes this a valuable platform on which to build local stewardship of marine resources, while raising awareness of the need to safeguard critically endangered largetooth sawfish.

ecology↗

bioRxiv2017

Complexity-Entropy maps as a tool for the characterization of the clinical electrophysiological evolution of patients under pharmacological treatment with psychotropic drugs

In the clinical electrophisiologic practice, the reading and comparing electroencephalographic (EEG) recordings some times is insufficient and take to much time. That is why in the last years it has begun to introduce new methods of EEG analysis, that give a better and faster understanding of the EEG dynamics and allow a rapid intervention in the patients treatment. Tools coming from the information theory or nonlinear system as an entropy and complexity have been shown to be a very good alternative to address this problem. In this work we introduce a novel method -the permutation Lempel-ziv complexity vs permutation entropy map. This method was applied to EEG of two patients with specific diagnosed pathologies during respective follow up processes of pharmacological changes in order to detect changes that are not evident with the usual inspection method. Our results show that the proposed method are useful for observing an evolutionary retrospective clinical effects of pharmacological interventions in both patients, and from these, to follow the clinical response to the proposed treatment.

neuroscience↗